Contacts of the strand formed by residues 611 - 620 (chain A) in PDB entry 4I1R
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 611 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384A LEU* 4.1 15.5 - - + -
607A GLU* 3.0 39.0 + - + +
608A PHE* 3.2 30.9 + - + +
609A SER 3.6 0.2 - - - -
610A ASN* 1.4 88.9 - - - +
612A MET* 1.3 61.1 + - - +
671A ARG* 3.4 43.1 - - + +
672A LEU 3.4 4.5 - - - +
673A SER* 3.3 22.4 - - - +
711A LEU* 4.0 2.8 - - - +
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Residues in contact with MET 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586A LEU* 4.0 9.2 - - + -
587A PRO* 4.0 19.3 - - - -
604A PHE* 3.8 21.3 - - + -
605A ALA 3.5 12.8 - - - +
610A ASN 4.2 0.4 - - - -
611A VAL* 1.3 74.8 - - - +
613A ILE* 1.4 70.5 + - - +
614A ILE* 3.7 30.7 - - + -
670A THR 4.0 0.2 - - - +
671A ARG* 3.5 1.1 - - - +
672A LEU* 2.7 56.6 + - + +
675A LEU* 4.2 8.3 - - + -
682A LEU* 3.9 14.4 - - + -
707A VAL* 4.6 1.3 - - + -
710A PRO* 4.0 14.6 - - + -
711A LEU* 3.7 13.2 - - + -
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Residues in contact with ILE 613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604A PHE* 3.5 5.2 - - - -
605A ALA* 2.9 39.0 + - + +
607A GLU* 3.2 39.5 - - + +
612A MET* 1.4 76.2 - - - +
614A ILE* 1.3 65.3 + - - +
615A TYR* 4.3 0.8 + - + -
651A PRO* 5.0 1.6 - - + -
656A SER* 3.7 21.8 - - - +
658A LEU* 3.7 19.3 - - + -
663A LEU* 4.2 16.8 - - + -
669A TYR* 3.7 32.3 - - + -
670A THR 3.6 5.8 - - - +
671A ARG* 4.2 11.0 - - + -
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Residues in contact with ILE 614 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602A LEU* 3.8 23.8 - - + -
603A GLY 3.7 3.1 - - - -
604A PHE* 3.9 13.2 - - + -
612A MET* 3.7 21.8 - - + -
613A ILE* 1.3 74.5 - - - +
615A TYR* 1.3 66.1 + - - +
616A THR* 4.9 0.7 - - + -
632A VAL* 4.3 22.8 - - + +
635A PHE* 3.7 17.9 - - + -
668A LEU 3.7 0.9 - - - +
669A TYR* 3.4 5.7 - - - -
670A THR* 2.7 40.0 + - - +
672A LEU* 3.6 34.8 - - + -
682A LEU* 5.0 0.7 - - + -
684A PHE* 4.8 7.9 - - + -
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Residues in contact with TYR 615 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589A SER* 5.4 2.1 + - - -
601A GLN* 3.6 9.3 - - + +
602A LEU* 3.5 6.2 - - - +
603A GLY* 2.8 57.4 + - - +
604A PHE* 3.5 27.4 + - - -
605A ALA* 4.8 0.4 - - + -
613A ILE* 4.8 2.0 - - + -
614A ILE* 1.3 76.3 - - - +
616A THR* 1.4 65.7 + - - +
617A SER* 5.3 3.1 - - - -
663A LEU* 3.8 28.9 - - + -
664A PRO* 3.4 35.8 - - + +
667A CYS* 3.9 13.0 - - + -
668A LEU 3.3 4.3 - - - +
669A TYR* 3.5 23.3 - + + -
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Residues in contact with THR 616 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600A ILE* 4.6 1.6 - - + -
601A GLN 3.4 6.5 - - - -
602A LEU* 4.8 7.9 - - + -
614A ILE* 4.9 1.6 - - + -
615A TYR* 1.4 78.0 - - - +
617A SER* 1.3 60.1 + - - +
629A ASP* 4.7 4.2 - - - +
630A ALA* 2.7 43.2 + - + +
632A VAL* 3.6 34.3 - - + -
647A ASN* 4.8 1.3 - - - +
666A HIS 4.4 0.5 - - - +
667A CYS* 3.2 6.6 - - - -
668A LEU* 3.0 38.7 + - - +
686A VAL* 5.2 1.3 - - + -
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Residues in contact with SER 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600A ILE* 3.4 8.8 - - - +
601A GLN* 2.8 53.1 + - - +
615A TYR* 4.3 3.5 - - - -
616A THR* 1.3 72.3 - - - +
618A ILE* 1.3 67.9 + - - +
619A VAL* 5.4 0.7 - - - +
629A ASP* 5.7 0.2 - - - -
630A ALA* 6.0 0.2 - - - -
664A PRO* 5.9 1.1 - - - +
665A LYS 5.4 0.9 - - - -
666A HIS 4.7 6.5 - - - -
667A CYS* 3.4 26.2 - - - -
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Residues in contact with ILE 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598A VAL* 4.3 7.0 - - + -
599A GLN 4.0 2.7 - - - -
600A ILE* 3.9 18.2 - - + -
617A SER* 1.3 78.9 + - - +
619A VAL* 1.3 61.6 + - - +
620A TYR 3.6 25.1 - - - +
621A LYS* 4.1 22.9 - - + +
628A CYS* 3.3 34.8 - - - +
629A ASP* 3.7 27.6 - - - +
630A ALA* 4.6 2.0 - - + +
666A HIS 5.3 2.9 + - - +
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Residues in contact with VAL 619 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591A CYS* 5.2 0.7 - - - -
599A GLN* 3.0 54.7 + - + +
600A ILE 4.5 5.2 - - - +
601A GLN* 4.6 16.8 - - + -
617A SER* 4.0 3.4 + - - +
618A ILE* 1.3 74.3 - - - +
620A TYR* 1.3 63.4 + - + +
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Residues in contact with TYR 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597A GLY* 4.3 15.9 - - - -
598A VAL* 3.3 24.9 - - - +
599A GLN* 3.4 20.8 + - + +
618A ILE* 3.6 4.8 - - - +
619A VAL* 1.3 84.7 - - + +
621A LYS* 1.3 69.5 + - - +
622A PRO* 4.2 24.4 - - + +
623A PRO* 5.3 4.5 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il